The present study examined the neural and behavioral correlates of selective stopping, a form of inhibition that has scarcely been investigated. The selectivity of the inhibitory process is needed when individuals have to deal with an environment filled with multiple stimuli, some of which require inhibition and some of which do not. The stimulus-selective stop-signal task has been used to explore this issue assuming that all participants interrupt their ongoing responses selectively to stop but not to ignore signals. However, recent behavioral evidence suggests that some individuals do not carry out the task as experimenters expect, since they seemed to interrupt their response non-selectively to both signals. In the present study, we detected and controlled the cognitive strategy adopted by participants (n = 57) when they performed a stimulus-selective stop-signal task before comparing brain activation between conditions. In order to determine both the onset and the end of the response cancellation process underlying each strategy and to fully take advantage of the precise temporal resolution of event-related potentials, we used a mass univariate approach. Source localization techniques were also employed to estimate the neural underpinnings of the effects observed at the scalp level. Our results from scalp and source level analysis support the behavioral-based strategy classification. Specific effects were observed depending on the strategy adopted by participants. Thus, when contrasting successful stop versus ignore conditions, increased activation was only evident for subjects who were classified as using a strategy whereby the response interruption process was selective to stop trials. This increased activity was observed during the P3 time window in several left-lateralized brain regions, including middle and inferior frontal gyri, as well as parietal and insular cortices. By contrast, in those participants who used a strategy characterized by stopping non-selectively, no activation differences between successful stop and ignore conditions were observed at the estimated time at which response interruption process occurs. Overall, results from the current study highlight the importance of controlling for the different strategies adopted by participants to perform selective stopping tasks before analyzing brain activation patterns.